[MMTK] Creating arbitrary molecules

michael.l.stoppelman.1 stoppeml at purdue.edu
Wed Jul 30 16:57:25 EDT 2003


I believe you need to add bonds between the atoms. You will have to dig
through the codebase a little. There is bond code in the Peptide chain
class that will give you a lead.

Good luck!
-mike

mike at stoppelman.com

> After a number of years of subscribing to the MMTK list, I've finally
> started to use MMTK for my day to day research. I'm tripping over a
> couple of minor bugs, and I was hoping that someone on the list could
> point out what I'm doing wrong.
>
> I can run several of the simple examples, particularly the ones that
> use molecules already in the database. However, when I try and create
> my own molecule from coordinates I run into trouble.
>
> Here's a trivial example:
> universe = InfiniteUniverse(Amber94ForceField())
>
> universe.addObject(Atom('O',position=Vector(0*Units.Ang,0*Units.Ang,0*Un
> its.Ang)))
> universe.addObject(Atom('H',position=Vector(1*Units.Ang,0*Units.Ang,0*Un
> its.Ang)))
> universe.addObject(Atom('H',position=Vector(0*Units.Ang,1*Units.Ang,0*Un
> its.Ang)))
>
> temperature = 298*Units.K
>
> universe.initializeVelocitiesToTemperature(temperature)
>
> integrator = VelocityVerletIntegrator(universe)
>
> integrator(steps=2000)
>
>
> If I replace the addObject calls with universe.molecule('water'), the
> example runs without problem. So I'm doing something wrong when I add
> the objects. Can anyone point out what I'm doing wrong?
>
> R.
>
> Rick Muller
> rmuller at sandia.gov
>
>
>
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